<PAGE>

[Confidential Treatment Requested. Confidential Portions of this Agreement
have been redacted and separately filed with the Commission.]

                                                                    EXHIBIT 10.3

                                                                  EXECUTION COPY

                FIRST AMENDMENT OF GENERAL PARTNERSHIP AGREEMENT

     This First Amendment of General Partnership Agreement is made and effective
as of September 25, 2000, by and between Becton Dickinson Venture LLC, a
Delaware limited liability company (the "Becton Partner"), and NanoVenture LLC,
a Delaware limited liability company (the "Nanogen Partner"). The Becton Partner
and the Nanogen Partner are hereinafter collectively referred to as the
"Partners".

     WHEREAS, the Partners formed a Delaware general partnership known as The
Nanogen/Becton Dickinson Partnership, as of October 1, 1997, pursuant to a
certain General Partnership Agreement dated as of October 1, 1997 (the
"Partnership Agreement"); and

     WHEREAS, the Partners desire to amend certain provisions of the Partnership
Agreement.

     NOW THEREFORE, for good and valuable consideration, the Partners hereby
agree to amend the Partnership Agreement as follows:

     1. The definitions of "Master Agreement" and "Research Agreement" contained
in Section 1.1 are each hereby deemed amended to refer to the fact that each has
been amended as of September 25, 2000.

     2. In Section 17, the Notice address for the Becton Partner is hereby
amended to read as follows (the address for required copies remaining
unchanged):

         If to the Becton Partner, to:

                           Becton Dickinson Venture LLC
                           c/o BD Biosciences
                           7 Loveton Circle
                           Sparks, Maryland  21152
                           Attn:   Vice President, Licensing and Patents

     3. Nothing contained in Section 12(b) shall operate or be construed to
prevent the Partners or their respective Affiliates from engaging in any of the
activities enumerated therein in competition with the Partnership Business, as
same is defined in the Master Agreement, dated as of October 1, 1997 by and
between the Partners and/or their Affiliates for all periods prior to amendment
of such Master Agreement on September 25, 2000; provided, however, that no
rights, express or implied, are hereby conferred on either Partner or its
respective Affiliates in any intellectual property rights of any of the
Partnership, either Partner or its respective Affiliates, other than those
provided in (a) the First Amendment of Collaborative Research and Development
and License Agreement, (b) the License Agreement and (c) the First Amendment to
License Agreement, all dated as of September 25, 2000 by and between the
Partners and/or the Affiliates.


<PAGE>

     4. A new Section 8.1(a)(vi) is hereby added as follows:

                           (vi)     In addition to the contributions set forth
                                    above in Sections 8.1(a)(i) through (v), the
                                    Becton Partner hereby agrees to make a *****
                                    contribution to the Partnership in the
                                    amount of Three Hundred Thousand Dollars
                                    ($300,000).

     5. Section 8.4 is amended by adding the following sentence to the end of
     the Section:

                           The contributions made by the Becton Partner pursuant
                           to Section 8.1(a)(vi) shall be used to ************
                           ***************************************************
                           ***************************************************
                           ********* pursuant to the Collaborative Research and
                           Development and License Agreement.

     IN WITNESS WHEREOF, the Partners have executed this First Amendment of
General Partnership Agreement through duly authorized representatives on the
dates set forth below, effective as of the date first written above.

BECTON DICKINSON VENTURE LLC

BY:  BECTON, DICKINSON AND COMPANY,
        SOLE MEMBER

        By:    /s/ VINCENT FORLENZA
            ---------------------------

Date: September 28, 2000
      ------------------------------


NANOVENTURE LLC

By:     /s/ HOWARD C. BIRNDORF
    --------------------------------

Date:    9/27/2000
      -------------------------------




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*** Confidential material redacted and separately filed with the Commission.